Editing Chloroplast (section)

=== Photosynthesis ===

{{main|Photosynthesis}}

One of the main functions of the chloroplast is its role in [[photosynthesis]], the process by which light is transformed into chemical energy, to subsequently produce food in the form of [[sugars]]. [[Water]] (H<sub>2</sub>O) and [[carbon dioxide]] (CO<sub>2</sub>) are used in photosynthesis, and sugar and [[oxygen]] (O<sub>2</sub>) are made, using [[light energy]]. Photosynthesis is divided into two stages—the [[light reactions]], where water is split to produce oxygen, and the [[dark reactions]], or [[Calvin cycle]], which builds sugar molecules from carbon dioxide. The two phases are linked by the energy carriers [[adenosine triphosphate]] (ATP) and [[nicotinamide adenine dinucleotide phosphate]] (NADP<sup>+</sup>).<ref name="Pearson-2009" /><ref name="Campbell-2006">{{cite book |last1=Campbell |first1=Neil A. |first2=Brad |last2=Williamson |first3=Robin J. |last3=Heyden | name-list-style=vanc |title=Biology: Exploring Life |publisher=Pearson Prentice Hall |year=2006 |location=Boston, Massachusetts |url=http://www.phschool.com/el_marketing.html |isbn=978-0-13-250882-7}}{{page needed|date=August 2013}}</ref>

==== Light reactions ====
{{main|Light reactions}}

{{Plain image with caption|File:Thylakoid membrane 3.svg|The [[light reactions]] of photosynthesis take place across the [[thylakoid]] membranes.<!-- [[Photosystem&nbsp;II]] is usually found in the appressed thylakoid membranes between stacked granal thylakoids, while [[photosystem&nbsp;I]] and [[ATP synthase]] is found in portions of the thylakoid membrane in contact with the stroma.-->|450px|right|top|triangle|#ccc}}

The light reactions take place on the thylakoid membranes. They take [[light energy]] and store it in [[NADPH]], a form of NADP<sup>+</sup>, and [[Adenosine triphosphate|ATP]] to fuel the [[dark reactions]].

===== Energy carriers =====

{{Main|Adenosine triphosphate|NADPH}}

ATP is the phosphorylated version of [[adenosine diphosphate]] (ADP), which stores energy in a cell and powers most cellular activities. ATP is the energized form, while ADP is the (partially) depleted form. NADP<sup>+</sup> is an electron carrier which ferries high energy electrons. In the light reactions, it gets [[redox reaction|reduced]], meaning it picks up electrons, becoming [[NADPH]].

===== Photophosphorylation =====

{{main|Photophosphorylation}}

Like mitochondria, chloroplasts use the [[potential energy]] stored in an [[Hydron (chemistry)|H<sup>+</sup>]], or hydrogen ion, gradient to generate ATP energy. The two [[photosystems]] capture light energy to energize [[electrons]] taken from [[water]], and release them down an [[electron transport chain]]. The [[Plastoquinone|molecules]] between the photosystems harness the electrons' energy to pump hydrogen ions into the thylakoid space, creating a [[concentration gradient]], with more hydrogen ions (up to a thousand times as many)<ref name="Campbell-2009b" /> inside the thylakoid system than in the stroma. The hydrogen ions in the thylakoid space then [[diffuse]] back down their concentration gradient, flowing back out into the stroma through [[ATP synthase]]. ATP synthase uses the energy from the flowing hydrogen ions to [[phosphorylate]] [[adenosine diphosphate]] into [[adenosine triphosphate]], or ATP.<ref name="Campbell-2009b" /><ref>{{cite journal | vauthors=Jagendorf AT, Uribe E | title=ATP formation caused by acid-base transition of spinach chloroplasts | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=55 | issue=1 | pages=170–7 | date=January 1966 | pmid=5220864 | pmc=285771 | doi=10.1073/pnas.55.1.170 | bibcode=1966PNAS...55..170J | doi-access=free }}</ref> Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there, in position to be used in the dark reactions.<ref name="Berg-2002b">{{cite book| first1=Jeremy M | last1=Berg | first2=John L | last2=Tymoczko | first3=Lubert | last3=Stryer | name-list-style=vanc |title=Biochemistry|year=2002|publisher=W. H. Freeman|location=New York, NY [u.a.]|isbn=0-7167-3051-0|pages=Section 19.4|edition=5. ed., 4. print.|url=https://archive.org/details/biochemistrychap00jere| url-access=registration }}</ref>

===== NADP<sup>+</sup> reduction =====

{{See also|Redox reaction}}

[[Electrons]] are often removed from the [[electron transport chains]] to charge [[NADP+|NADP<sup>+</sup>]] with electrons, [[reduction reaction|reducing]] it to [[NADPH]]. Like ATP synthase, [[ferredoxin—NADP+ reductase|ferredoxin-NADP<sup>+</sup> reductase]], the enzyme that reduces NADP<sup>+</sup>, releases the NADPH it makes into the stroma, right where it is needed for the dark reactions.<ref name="Berg-2002b" />

Because NADP<sup>+</sup> reduction removes electrons from the electron transport chains, they must be replaced—the job of [[photosystem II]], which splits [[water]] molecules (H<sub>2</sub>O) to obtain the electrons from its [[hydrogen atoms]].<ref name="Campbell-2009b" /><ref name="Pearson-2009">{{cite book|title=Biology—Concepts and Connections|year=2009|publisher=Pearson|pages=108–118}}</ref>

===== Cyclic photophosphorylation =====

{{Main|Cyclic photophosphorylation}}

While [[photosystem II]] [[photolyzes]] water to obtain and energize new electrons, [[photosystem I]] simply reenergizes depleted electrons at the end of an electron transport chain. Normally, the reenergized electrons are taken by NADP<sup>+</sup>, though sometimes they can flow back down more H<sup>+</sup>-pumping electron transport chains to transport more hydrogen ions into the thylakoid space to generate more ATP. This is termed [[cyclic photophosphorylation]] because the electrons are recycled. Cyclic photophosphorylation is common in [[C4 plants|{{C4}} plants]], which need more [[Adenosine triphosphate|ATP]] than [[NADPH]].<ref name="Campbell-2009d" />

==== Dark reactions ====
{{Main|Dark reactions}}

{{Plain image with caption|File:Calvin-cycle4.svg|'''The Calvin cycle''' ''(Interactive diagram)'' The [[Calvin cycle]] incorporates carbon dioxide into sugar molecules.|435px|right|top|triangle|#ccc|image override=}}
<!--{{Calvin cycle}}-->

The [[Calvin cycle]], also known as the [[dark reactions]], is a series of biochemical reactions that fixes [[CO2|CO<sub>2</sub>]] into [[Glyceraldehyde 3-phosphate|G3P]] sugar molecules and uses the energy and electrons from the [[Adenosine triphosphate|ATP]] and [[NADPH]] made in the light reactions. The Calvin cycle takes place in the stroma of the chloroplast.<ref name="Campbell-2009d" />

While named ''"the dark reactions"'', in most plants, they take place in the light, since the dark reactions are dependent on the products of the light reactions.<ref name="Campbell-2009g" />

===== Carbon fixation and G3P synthesis =====

The Calvin cycle starts by using the enzyme [[RuBisCO]] to fix CO<sub>2</sub> into five-carbon [[Ribulose bisphosphate]] (RuBP) molecules. The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called [[3-phosphoglyceric acid]], or 3-PGA.
The [[Adenosine triphosphate|ATP]] and [[NADPH]] made in the light reactions is used to convert the 3-PGA into [[glyceraldehyde-3-phosphate]], or G3P sugar molecules. Most of the G3P molecules are recycled back into RuBP using energy from more ATP, but one out of every six produced leaves the cycle—the end product of the dark reactions.<ref name="Campbell-2009d" />

===== Sugars and starches =====

{{Plain image with caption|File:Saccharose2.svg|Sucrose is made up of a [[glucose]] monomer (left), and a [[fructose]] monomer (right).|width=220px|align=left|caption position=top|triangle=triangle|triangle color=#aaa}}

Glyceraldehyde-3-phosphate can double up to form larger sugar molecules like [[glucose]] and [[fructose]]. These molecules are processed, and from them, the still larger [[sucrose]], a [[disaccharide]] commonly known as table sugar, is made, though this process takes place outside of the chloroplast, in the [[cytoplasm]].<ref name="Berg-2002a">{{cite book| first1=Jeremy M | last1=Berg | first2=John L | last2=Tymoczko | first3=Lubert | last3=Stryer | name-list-style=vanc |title=Biochemistry|year=2002|publisher=W. H. Freeman|location=New York, NY [u.a.]|isbn=0-7167-3051-0|pages=Section 20.1|edition=5. ed., 4. print.|url=https://archive.org/details/biochemistrychap00jere| url-access=registration }}</ref>

Alternatively, glucose [[monomers]] in the chloroplast can be linked together to make [[starch]], which accumulates into the [[chloroplast starch granule|starch grains]] found in the chloroplast.<ref name="Berg-2002a" />
Under conditions such as high atmospheric CO<sub>2</sub> concentrations, these starch grains may grow very large, distorting the grana and thylakoids. The starch granules displace the thylakoids, but leave them intact.<ref name="Wample-1983" />
Waterlogged [[root]]s can also cause [[starch]] buildup in the chloroplasts, possibly due to less [[sucrose]] being exported out of the chloroplast (or more accurately, the [[plant cell]]). This depletes a plant's [[free phosphate]] supply, which indirectly stimulates chloroplast starch synthesis.<ref name="Wample-1983">{{cite journal | vauthors=Wample RL, Davis RW | title=Effect of Flooding on Starch Accumulation in Chloroplasts of Sunflower (Helianthus annuus L.) | journal=Plant Physiology | volume=73 | issue=1 | pages=195–8 | date=September 1983 | pmid=16663176 | pmc=1066435 | doi=10.1104/pp.73.1.195 }}</ref>
While linked to low photosynthesis rates, the starch grains themselves may not necessarily interfere significantly with the efficiency of photosynthesis,<ref>{{cite journal| vauthors=Carmi A, Shomer I |year=1979|title=Starch Accumulation and Photosynthetic Activity in Primary Leaves of Bean (''Phaseolus vulgaris'' L.)|journal=Annals of Botany|volume=44|issue=4|pages=479–484|doi=10.1093/oxfordjournals.aob.a085756 }}</ref> and might simply be a side effect of another photosynthesis-depressing factor.<ref name="Wample-1983" />

===== Photorespiration =====

[[Photorespiration]] can occur when the oxygen concentration is too high. RuBisCO cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O<sub>2</sub> instead of CO<sub>2</sub> to [[RuBP]]. This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO<sub>2</sub>, and produces no sugar. It can waste up to half the carbon fixed by the Calvin cycle.<ref name="Pearson-2009" /> Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. These mechanisms are called [[carbon dioxide concentrating mechanism]]s, or CCMs. These include [[Crassulacean acid metabolism]], [[C4 carbon fixation|{{C4}} carbon fixation]],<ref name="Pearson-2009" /> and [[pyrenoid]]s. Chloroplasts in {{C4}} plants are notable as they exhibit a distinct [[#Specialized chloroplasts in C4 plants|chloroplast dimorphism]].